Rodent Studies

This example demonstrates how to perform a DBS simulation in a rodent brain using OSS-DBSv2.

MRI and DTI data are openly available, for example from the Johnson et al.rat brain atlas:

Publication: Johnson, G. Allan, et al. A multicontrast MR atlas of the Wistar rat brain. NeuroImage, 242 (2021), 118470. DOI: https://doi.org/10.1016/j.neuroimage.2021.118470
Original Dataset: https://civmvoxport.vm.duke.edu/voxbase/studyhome.php?studyid=754/
License: https://creativecommons.org/licenses/by-nc-sa/3.0/
Author/Creator: Johnson, G. Allan, et al.

After downloading the dataset, the segmented MRI (segmask.nii.gz) and the normalized DTI can be used in OSS-DBSv2 as follows:

"MaterialDistribution": {
  "MRIPath": "./input_files/segmask.nii.gz",
  "MRIMapping": {
    "Unknown": 0,
    "CSF": 3,
    "White matter": 2,
    "Gray matter": 1,
    "Blood": 4
  },
  "DiffusionTensorActive": false,
  "DTIPath": ""
},

Rodent Electrodes

In addition to clinical DBS electrodes, OSS-DBSv2 includes dedicated electrode models for small rodent studies. A complete list is available in the electrode documentation.

In this example, a SNEX100 electrode is implanted cranially into the region of the subthalamic nucleus (STN). The electrode has two contacts, so either bipolar or monopolar stimulation can be used. Below a configuration for monopolar stimulation with 1 V at contact 1 is shown. As simplification, the outer boundary of the brain region is treated as ground. Since most rodent electrodes do not feature directional contacts, no orientation needs to be specified.

"Electrodes": [
  {
    "Name": "MicroProbesSNEX100",
    "Rotation[Degrees]": 0,
    "Direction": {"x[mm]": 2.23, "y[mm]": 5.07, "z[mm]": 3.99},
    "TipPosition": {"x[mm]": 14.59, "y[mm]": -14.74, "z[mm]": -9.06},
    "Contacts": [
      {
        "Contact_ID": 1,
        "Active": true,
        "Voltage[V]": 1.0,
        "Floating": false
      },
      {
        "Contact_ID": 2,
        "Active": false,
        "Voltage[V]": 0.0,
        "Floating": true
      }
    ]
  }
],
"Surfaces": [
  {
    "Name": "BrainSurface",
    "Active": true,
    "Voltage[V]": 0.0,
    "Floating": false
  }
],

The Surfaces block sets boundary conditions on the outer brain surface. Here it is used to treat the brain boundary as a grounded electrode (0 V, active), providing the return path for monopolar stimulation. This is a common simplification in rodent studies where the skull or a distant return electrode acts as ground. The surface name BrainSurface matches the default name assigned to the outer boundary by BrainGeometry.

Estimate Stimulation Volume

To the stimulation volume a point model around the electrode tip is created. Therefore, the Lattice option is activated and the location and number of points specified.

"PointModel": {
  "Pathway": {
    "Active": false,
    "FileName": ""
  },
  "Lattice": {
    "Active": true,
    "Center":  {"x[mm]": 14.59, "y[mm]": -14.74, "z[mm]": -9.06},
    "Shape": {"x": 20, "y": 20, "z": 20},
    "Direction": {"x[mm]": 2.23, "y[mm]": 5.07, "z[mm]": 3.99},
    "PointDistance[mm]": 0.5
  }
},

The results are stored in the specified OutputPath directory after running the simulation.